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Alan
9
cnmodel/decorator/__init__.py
Executable file
9
cnmodel/decorator/__init__.py
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#!/usr/bin/python
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#
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# Channel decorator class for cnmodel
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#
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# Paul B. Manis, Ph.D. January 2016
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#
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from neuron import h
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from .decorator import Decorator
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392
cnmodel/decorator/decorator.py
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392
cnmodel/decorator/decorator.py
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from __future__ import print_function
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__author__ = "pbmanis"
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"""
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Decorator:
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A class to insert biophysical mechanisms into a model.
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This function attempts to automatically decorate a hoc-imported model set of sections
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with appropriate conductances.
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The class takes as input the object hf, which is an instance of morphology
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It also takes the cellType, a string that directs how conductances should be inserted.
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"""
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import string
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import numpy as np
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import cnmodel.util as nu
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from cnmodel.util import Params
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class Decorator:
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def __init__(self, cell, parMap=None, verify=False):
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cellType = cell.type.lower()
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self.channelInfo = Params(
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newCm=1.0,
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newRa=150.0, # standard value
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newg_leak=0.000004935,
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eK_def=-85,
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eNa_def=50,
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ca_init=70e-6, # free calcium in molar
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v_init=-80, # mV
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pharmManip={
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"TTX": False,
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"ZD": False,
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"Cd": False,
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"DTX": False,
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"TEA": False,
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"XE": False,
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},
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cellType=cell.status["cellClass"],
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modelType=cell.status["modelType"],
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modelName=cell.status["modelName"],
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distanceMap=cell.hr.distanceMap,
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parMap=parMap,
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)
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self.excludeMechs = [] # ['ihvcn', 'kht', 'klt', 'nav11']
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print("modelType in dec: ", cell.status["modelType"])
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print("modelName in dec is ", cell.status["modelName"])
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print("cell type in dec: ", cellType)
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cell.channel_manager(
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modelName=cell.status["modelName"], modelType=cell.status["modelType"]
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)
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# print 'Cell: \n', dir(cell)
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# print 'mechanisms: ', cell.hr.mechanisms
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# gmapper allows us tor remap the names of mechanisms and their conductance names, which may
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# vary in the mod files.
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# The versions in the mechanisms directory here have been systematized, but this
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# dictionary may help when adding other conductances.
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self.gbar_mapper = {
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"nacn": "gbar",
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"kht": "gbar",
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"klt": "gbar",
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"leak": "gbar",
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"ihvcn": "gbar",
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"jsrna": "gbar",
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"nav11": "gbar",
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"nacncoop": "gbar",
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"hcnobo": "gbar",
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}
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self.erev_mapper = {
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"nacn": "ena",
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"kht": "ek",
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"klt": "ek",
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"leak": "erev",
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"ihvcn": "eh",
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"jsrna": "ena",
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"nav11": "ena",
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"nacncoop": "ena",
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"hcnobo": "eh",
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}
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self.vshift_mapper = {
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"nacn": None,
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"kht": None,
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"klt": None,
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"leak": None,
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"ihvcn": None,
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"jsrna": None,
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"nav11": "vsna",
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"nacncoop": "vsna",
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"hcnobo": None,
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}
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self._biophys(cell, verify=verify)
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print(
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"\033[1;31;40m Decorator: Model Decorated with channels (if this appears more than once per cell, there is a problem)\033[0m"
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)
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def _biophys(self, cell, verify=False):
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"""
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Inputs: run parameter structure, model parameter structure
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verify = True to run through the inserted mechanisms and see that they are really there.
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Outputs: None
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Action: Channel insertion into model
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Side Effects:
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Sets conductances in every different kind of section
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Does not update any class variables (via self).
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original hoc code: Paul B. Manis, Ph.D.
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25 Sept. 2007
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Modified to use gca for HH formulation of calcium current
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14 Oct 2007
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converted for Python, 17 Oct 2012 (PB Manis)
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modified to use new hf hoc_reader class to access section types and mechanisms 10-14 Feb 2014 pbmanis
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"""
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# check to see if we already did this
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# createFlag = False
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cellType = self.channelInfo.cellType
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parMap = self.channelInfo.parMap
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dmap = self.channelInfo.distanceMap
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if self.channelInfo is None:
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raise Exception("biophys - no parameters or info passed!")
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if verify:
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print(
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"Biophys: Inserting channels as if cell type is {:s} with modelType {:s}".format(
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cellType, self.channelInfo.modelType
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)
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)
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cell.hr.mechanisms = []
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for s in list(cell.hr.sec_groups.keys()):
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sectype = self.remapSectionType(s.rsplit("[")[0])
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if sectype not in cell.channelMap.keys():
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print(
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"encountered unknown section group type: %s Not decorating"
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% sectype
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)
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print("channels in map: ", cell.channelMap.keys())
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continue
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# print 'Biophys: Section type: ', sectype, 'from: ', s
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# print sectype
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# print 'channel mapping keys: ', cell.channelMap[sectype].keys()
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# here we go through all themechanisms in the ionchannels table for this cell and compartment type
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# note that a mechanism may have multiple parameters in the table (gbar, vshft), so we:
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# a. only insert the mechanism once
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# b. only adjust the relevant parameter
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for mechname in list(cell.channelMap[sectype].keys()):
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mech = mechname.split("_")[0] # get the part before the _
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parameter = mechname.split("_")[1] # and the part after
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if mech not in self.gbar_mapper.keys():
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print("Mechanism %s not found? " % mech)
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continue
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if mech in self.excludeMechs:
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continue
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if verify:
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print(
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"Biophys: section group: {:s} insert mechanism: {:s} at {:.8f}".format(
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s, mech, cell.channelMap[sectype][mech]
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)
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)
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if mech not in cell.hr.mechanisms:
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cell.hr.mechanisms.append(
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mech
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) # just add the mechanism to our list
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x = nu.Mechanism(mech)
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if cell.hr.sec_groups[s] == set():
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continue # no sections of this type
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for sec in cell.hr.sec_groups[
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s
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]: # insert into all the sections of this type (group)
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try:
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x.insert_into(cell.hr.get_section(sec))
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except:
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raise ValueError(
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"Failed with mech: %s " % mech
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) # fail if cannot insert.
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if verify:
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print(" inserted %s into section " % mech, sec)
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gbar_setup = None
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gbar = 0.0
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if parameter == "gbar":
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gbar = self.gbarAdjust(
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cell, sectype, mechname, sec
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) # map density by location/distance
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gbar_setup = "%s_%s" % (
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self.gbar_mapper[mech],
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mech,
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) # map name into .mod file name
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# if parMap is not None and mech in parMap.keys(): # note, this allows parmap to have elements BESIDES mechanisms
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# if verify:
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# print 'parMap[mech]', mech, parMap[mech], gbar,
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# gbar = gbar * parMap[mech] # change gbar here...
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# if verify:
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print("####### new gbar: ", gbar)
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vshift_setup = None
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vshift = 0.0
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# print 'Parameter: ', parameter, mech, self.vshift_mapper[mech]
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if parameter == "vshift" and self.vshift_mapper[mech] is not None:
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vshift_setup = "%s_%s" % (
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self.vshift_mapper[mech],
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mech,
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) # map voltage shift
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vshift = cell.channelMap[sectype][mechname]
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print(
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"********* mech: gbar, vshift: ", gbar, vshift, vshift_setup
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)
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exit()
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cell.hr.h.Ra = self.channelInfo.newRa
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for sec in cell.hr.sec_groups[
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s
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]: # now set conductances and other parameters as requested
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cell.hr.get_section(sec).Ra = self.channelInfo.newRa # set Ra here
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if gbar_setup is not None:
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setattr(
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cell.hr.get_section(sec), gbar_setup, gbar
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) # set conductance magnitude
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# print('gbar_setup: %s %s' % (sectype, gbar_setup), gbar)
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if vshift_setup is not None:
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try:
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setattr(
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cell.hr.get_section(sec), vshift_setup, vshift
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) # set conductance magnitude
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except:
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print(dir(cell.hr.get_section(sec)))
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raise ValueError(
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" cannot set mechanism attribute %s ... %s "
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% (vshift_setup, vshift)
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)
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# print('vshift_setup: %s %s' % (sectype, vshift_setup), vshift)
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if hasattr(
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cell, "channelErevMap"
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): # may not always have this mapping
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secobj = cell.hr.get_section(
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sec
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) # get the NEURON section object
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mechsinsec = cell.get_mechs(
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secobj
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) # get list of mechanisms in this section
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if (
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mech in mechsinsec
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): # confirm that the mechanism is really there
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setrev = (
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False
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) # We try two ways for different mechanisms - just flag it
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try:
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setattr(
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secobj,
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self.erev_mapper[mech],
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cell.channelErevMap[sectype][mech],
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)
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setrev = True
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continue # don't bother with second approach
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except:
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raise ValueError("erev set failed")
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pass # no error
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try:
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setattr(
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secobj(),
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self.erev_mapper[mech] + "_" + mech,
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cell.channelErevMap[sectype][mech],
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)
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setrev = True
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except:
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raise ValueError("Erev2 set failed")
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pass # no error report
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if (
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not setrev
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): # here is our error report - soft, not crash.
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print(
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"Failed to set reversal potential in section %s for mechanism %s"
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% (sec, mech)
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)
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# if mech in mechinsec and mech in self.vshift_mapper.keys():
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# try:
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# setattr(secobj, self.vshift_mapper[mech], cell.channelVshiftMap[sectype][mech])
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# except:
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# raise ValueError('Failed to set vshift for mech: %s sectpe: %s' % (mech, sectype[mech]))
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if verify:
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self.channelValidate(cell)
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return cell
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def gbarAdjust(self, cell, sectype, mech, sec):
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gbar = cell.channelMap[sectype][mech]
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gbar_orig = gbar
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if sectype not in cell.distMap.keys(): # no map for this section type
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return gbar
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elif mech not in cell.distMap[sectype].keys():
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return gbar
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# mecanism exists in the distMap, so we will map gbar to distance from soma
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method = cell.distMap[sectype][mech]["gradient"] # grab the type
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gminf = cell.distMap[sectype][mech]["gminf"]
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rate = cell.distMap[sectype][mech]["lambda"]
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# print('sectype: %s mech: %s method: %s rate: %s' % (sectype, mech, method, rate))
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if method == "flat":
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return gbar
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if sec in self.channelInfo.distanceMap.keys():
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dist = self.channelInfo.distanceMap[sec]
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else: # the sec should be in the map, but there could be a coding error that would break that relationship
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raise NameError(
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"gbarAdjust in channel_decorate.py: section %s not in distance map"
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% sec
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)
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if method == "linear": # rate is "half" point drop
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# print('doing linear, orig gbar: ', gbar)
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gbar = gbar - dist * (gbar - gminf) / rate
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if gbar < 0.0:
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gbar = 0.0 # clip
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# print('sec dist: %f final gbar: %f' % (dist, gbar))
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elif method in ["exp", "expdown"]:
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gbar = (gbar - gminf) * np.exp(-dist / rate) + gminf
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if gbar < 0.0:
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gbar = 0.0
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# print 'gbaradjust: orig/adj: ', gbar_orig, gbar, method, dist, sectype
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return gbar
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def channelValidate(self, cell, verify=False):
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"""
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verify mechanisms insertions -
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go through all the groups, and find inserted conductances and their values
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print the results to the terminal
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"""
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print("\nChannel Validation")
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print(" Looking for sec_groups: ", sorted(cell.hr.sec_groups.keys()))
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print(" Available Channel Maps: ", sorted(cell.channelMap.keys()))
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secstuff = {}
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for s in list(cell.hr.sec_groups.keys()):
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sectype = self.remapSectionType(s.rsplit("[")[0])
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if sectype not in cell.channelMap.keys():
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if sectype in ["undefined"]: # skip undefined sections
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continue
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print(
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"\033[1;31;40m Validation: encountered unknown section group type: %s Cannot Validate"
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% sectype
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)
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print("Cell morphology file: %s \033[0m" % cell.morphology_file)
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continue
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# print 'Validating Section: %s' % s
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for mech in list(cell.channelMap[sectype].keys()):
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if mech not in self.gbar_mapper.keys():
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continue
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if mech in self.excludeMechs:
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continue
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if verify:
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print(
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"\tSection: %-15ss found mechanism: %-8ss at %.5f"
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% (s, mech, cell.channelMap[sectype][mech])
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)
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x = nu.Mechanism(
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mech
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) # , {gmapper[mech]: self.channelMap[cellType][sectype][mech]})
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setup = "%s_%s" % (self.gbar_mapper[mech], mech)
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for sec in cell.hr.sec_groups[s]:
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bar = getattr(cell.hr.get_section(sec), setup)
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# print 'mech', mech
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# print 'bar: ', bar
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try:
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Erev = getattr(cell.hr.get_section(sec), self.erev_mapper[mech])
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except:
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Erev = -999.0
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# print 'erev: ', Erev
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if sec in secstuff.keys():
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secstuff[sec] += ", g_%s = %g [%.1f]" % (mech, bar, Erev)
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else:
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secstuff[sec] = "(%10s) g_%-6s = %g [%.1f] " % (
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sectype,
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mech,
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bar,
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Erev,
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)
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if verify:
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for i, k in enumerate(secstuff.keys()):
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print("**%-20s " % k, secstuff[k])
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def remapSectionType(self, sectype):
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if sectype in ["AXON_0"]:
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sectype = "axon"
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if sectype in ["initseg", "initialsegment"]:
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sectype = "initialsegment"
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if sectype in ["dendscaled_0", "dendscaled_1", "dendscaled_2", "dendrite"]:
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sectype = "dendrite"
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if sectype in ["apical_dendrite"]:
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sectype = "secondarydendrite"
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return sectype
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